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- PDB-5jo2: Crystal structure of abscisic acid-bound abscisic acid receptor P... -

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Basic information

Entry
Database: PDB / ID: 5jo2
TitleCrystal structure of abscisic acid-bound abscisic acid receptor PYL3 in complex with type 2C protein phosphatase HAB1
Components
  • Abscisic acid receptor PYL3
  • Protein phosphatase 2C 16
KeywordsSIGNALING PROTEIN/Hydrolase / ABA receptor / PYR/PYL / PYL3 / SIGNALING PROTEIN-Hydrolase complex
Function / homology
Function and homology information


protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / signaling receptor activity / protein homodimerization activity / identical protein binding ...protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / signaling receptor activity / protein homodimerization activity / identical protein binding / metal ion binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C / Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. ...PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C / Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 4-Layer Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-A8S / Protein phosphatase 2C 16 / Abscisic acid receptor PYL3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsWeng, J.K. / Noel, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell / Year: 2016
Title: Co-evolution of Hormone Metabolism and Signaling Networks Expands Plant Adaptive Plasticity.
Authors: Weng, J.K. / Ye, M. / Li, B. / Noel, J.P.
History
DepositionMay 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Abscisic acid receptor PYL3
B: Protein phosphatase 2C 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0485
Polymers57,7352
Non-polymers3133
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-27 kcal/mol
Surface area21550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.330, 75.310, 169.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Abscisic acid receptor PYL3 / PYR1-like protein 3 / Regulatory components of ABA receptor 13


Mass: 20601.514 Da / Num. of mol.: 1 / Fragment: UNP residues 24-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYL3, RCAR13, At1g73000, F3N23.20 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SSM7
#2: Protein Protein phosphatase 2C 16 / AtPP2C16 / AtP2C-HA / Protein HYPERSENSITIVE TO ABA 1 / Protein phosphatase 2C HAB1 / PP2C HAB1


Mass: 37133.531 Da / Num. of mol.: 1 / Fragment: UNP residues 172-506
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HAB1, P2C-HA, At1g72770, F28P22.4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9CAJ0, protein-serine/threonine phosphatase
#3: Chemical ChemComp-A8S / (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid / (+)-abscisic acid / (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxo-2-cyclohexen-1-yl]-3-methyl-2,4-pentadienoic acid / Abscisic acid


Mass: 264.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H20O4 / Comment: hormone*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M Mg(NO3)2, 0.1 M Tris-HCl pH 8.0, 28% (v/v) PEG3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.42→56.251 Å / Num. obs: 32269 / % possible obs: 84.5 % / Redundancy: 1.7 % / Net I/σ(I): 6.12

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→56.251 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0.89 / Phase error: 31.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2546 1616 5.01 %
Rwork0.2094 --
obs0.2117 32269 75.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.42→56.251 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3753 0 21 19 3793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033840
X-RAY DIFFRACTIONf_angle_d0.7765193
X-RAY DIFFRACTIONf_dihedral_angle_d15.5121436
X-RAY DIFFRACTIONf_chiral_restr0.029589
X-RAY DIFFRACTIONf_plane_restr0.003667
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4201-2.49130.318720.34841407X-RAY DIFFRACTION42
2.4913-2.57170.4214850.34131398X-RAY DIFFRACTION42
2.5717-2.66360.3257790.33291451X-RAY DIFFRACTION43
2.6636-2.77020.3787800.3461321X-RAY DIFFRACTION40
2.7702-2.89630.29751180.30932440X-RAY DIFFRACTION72
2.8963-3.0490.36791650.28283213X-RAY DIFFRACTION95
3.049-3.240.28211690.2493250X-RAY DIFFRACTION96
3.24-3.49020.2771700.22273232X-RAY DIFFRACTION96
3.4902-3.84130.2341730.19453223X-RAY DIFFRACTION96
3.8413-4.3970.25451710.17463244X-RAY DIFFRACTION96
4.397-5.5390.2121690.16493222X-RAY DIFFRACTION95
5.539-56.26630.20551650.18533252X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 20.0699 Å / Origin y: -35.9335 Å / Origin z: -21.7919 Å
111213212223313233
T0.2789 Å2-0.0249 Å2-0.008 Å2-0.2641 Å2-0.0069 Å2--0.24 Å2
L0.2896 °20.319 °2-0.047 °2-1.3537 °2-0.7361 °2--0.6698 °2
S0.0767 Å °-0.1031 Å °0.0176 Å °0.3602 Å °-0.0832 Å °-0.0798 Å °-0.3037 Å °-0.0699 Å °-0.0003 Å °
Refinement TLS groupSelection details: all

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